I know Stars and Party allow final table deal making, Blue Square don"t not too sure on others.
On Stars all players left sit out, discuss deal and let their hands fold to BB whilst discussing. Once an agreement has been reached in principal somone e-mails Stars Customer Support with the words "URGENT FINAL TABLE CHOP ID No xxxxxxxx"
A ManagerHost will then officially pause the game, come onto the chat and find out what has been agreed or assist in any calcualtions to accomodate a deal. All players have to agree and they then re-start tournie to play out for whatever monies are left over or for tournament leader board points.
Initially the original payment goes into your account, but as soon as the tournament officially finishes the accounts amend automatically to the agreed deal amounts.
It"s pretty painless and tbh, I am starting to gravitate towards sites that offer this facility, because it"s all a part of the game.